diff --git a/tests/test_polyclonalaverage.ipynb b/tests/test_polyclonalaverage.ipynb
index 2dd78e3c..e574dd51 100644
--- a/tests/test_polyclonalaverage.ipynb
+++ b/tests/test_polyclonalaverage.ipynb
@@ -22,13 +22,6 @@
    "execution_count": 1,
    "id": "5935c6e6-a5ae-4d73-8f80-03c7d36775f0",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:12.123716Z",
-     "iopub.status.busy": "2023-07-19T19:40:12.123318Z",
-     "iopub.status.idle": "2023-07-19T19:40:14.431939Z",
-     "shell.execute_reply": "2023-07-19T19:40:14.430678Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:12.123687Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -189,13 +182,6 @@
    "execution_count": 2,
    "id": "0667e765-d0d7-40fc-b21b-c2da5fedec23",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:14.441393Z",
-     "iopub.status.busy": "2023-07-19T19:40:14.440939Z",
-     "iopub.status.idle": "2023-07-19T19:40:14.705332Z",
-     "shell.execute_reply": "2023-07-19T19:40:14.704549Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:14.441368Z"
-    },
     "tags": []
    },
    "outputs": [],
@@ -216,13 +202,6 @@
    "execution_count": 3,
    "id": "c6396f53-82f2-4fcf-bd2d-b6f0c03f8d7f",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:14.709597Z",
-     "iopub.status.busy": "2023-07-19T19:40:14.709229Z",
-     "iopub.status.idle": "2023-07-19T19:40:14.819708Z",
-     "shell.execute_reply": "2023-07-19T19:40:14.819088Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:14.709561Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -269,83 +248,83 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>2</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.877</td>\n",
        "      <td>A</td>\n",
-       "      <td>0</td>\n",
+       "      <td>1</td>\n",
        "      <td>A</td>\n",
        "      <td>0</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.770</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
        "      <td>1</td>\n",
-       "      <td>0.877</td>\n",
+       "      <td>0.997</td>\n",
        "      <td>A</td>\n",
-       "      <td>1</td>\n",
+       "      <td>2</td>\n",
        "      <td>A</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.770</td>\n",
+       "      <td>0.994</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>2</td>\n",
-       "      <td>1.000</td>\n",
-       "      <td>A</td>\n",
        "      <td>1</td>\n",
+       "      <td>0.999</td>\n",
+       "      <td>B</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.999</td>\n",
+       "      <td>0.998</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
        "      <td>1</td>\n",
-       "      <td>0.997</td>\n",
-       "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0.893</td>\n",
+       "      <td>B</td>\n",
+       "      <td>1</td>\n",
        "      <td>A</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.994</td>\n",
+       "      <td>0.798</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>5</th>\n",
        "      <td>2</td>\n",
-       "      <td>0.992</td>\n",
+       "      <td>1.000</td>\n",
        "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.984</td>\n",
+       "      <td>1.000</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>6</th>\n",
+       "      <td>2</td>\n",
+       "      <td>1.000</td>\n",
+       "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.999</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.998</td>\n",
+       "      <td>0.999</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>7</th>\n",
        "      <td>2</td>\n",
        "      <td>0.992</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
+       "      <td>A</td>\n",
+       "      <td>2</td>\n",
        "      <td>A</td>\n",
        "      <td>0</td>\n",
        "      <td>0.984</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>8</th>\n",
-       "      <td>1</td>\n",
-       "      <td>0.893</td>\n",
+       "      <td>2</td>\n",
+       "      <td>0.992</td>\n",
        "      <td>B</td>\n",
-       "      <td>1</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.798</td>\n",
+       "      <td>0.984</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>9</th>\n",
@@ -369,83 +348,83 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>11</th>\n",
-       "      <td>2</td>\n",
+       "      <td>1</td>\n",
        "      <td>1.000</td>\n",
        "      <td>A</td>\n",
-       "      <td>0</td>\n",
+       "      <td>1</td>\n",
        "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.999</td>\n",
+       "      <td>1.000</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>12</th>\n",
        "      <td>1</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.929</td>\n",
        "      <td>A</td>\n",
-       "      <td>1</td>\n",
+       "      <td>2</td>\n",
        "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.863</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>13</th>\n",
-       "      <td>2</td>\n",
-       "      <td>1.000</td>\n",
-       "      <td>A</td>\n",
        "      <td>1</td>\n",
+       "      <td>-0.289</td>\n",
+       "      <td>B</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.084</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>14</th>\n",
        "      <td>1</td>\n",
-       "      <td>0.929</td>\n",
-       "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0.998</td>\n",
+       "      <td>B</td>\n",
+       "      <td>1</td>\n",
        "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.863</td>\n",
+       "      <td>0.996</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>15</th>\n",
        "      <td>2</td>\n",
-       "      <td>0.999</td>\n",
+       "      <td>1.000</td>\n",
        "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.998</td>\n",
+       "      <td>0.999</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>16</th>\n",
+       "      <td>2</td>\n",
+       "      <td>1.000</td>\n",
+       "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>-0.289</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.084</td>\n",
+       "      <td>1.000</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>17</th>\n",
        "      <td>2</td>\n",
-       "      <td>0.966</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
+       "      <td>0.999</td>\n",
+       "      <td>A</td>\n",
+       "      <td>2</td>\n",
        "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.933</td>\n",
+       "      <td>0.998</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>18</th>\n",
-       "      <td>1</td>\n",
-       "      <td>0.998</td>\n",
+       "      <td>2</td>\n",
+       "      <td>0.966</td>\n",
        "      <td>B</td>\n",
-       "      <td>1</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.996</td>\n",
+       "      <td>0.933</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>19</th>\n",
@@ -469,83 +448,83 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>21</th>\n",
-       "      <td>2</td>\n",
-       "      <td>0.992</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.929</td>\n",
        "      <td>A</td>\n",
-       "      <td>0</td>\n",
+       "      <td>1</td>\n",
        "      <td>A</td>\n",
        "      <td>2</td>\n",
-       "      <td>0.984</td>\n",
+       "      <td>0.863</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>22</th>\n",
        "      <td>1</td>\n",
-       "      <td>0.929</td>\n",
+       "      <td>1.000</td>\n",
        "      <td>A</td>\n",
-       "      <td>1</td>\n",
+       "      <td>2</td>\n",
        "      <td>A</td>\n",
        "      <td>2</td>\n",
-       "      <td>0.863</td>\n",
+       "      <td>1.000</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>23</th>\n",
-       "      <td>2</td>\n",
-       "      <td>0.999</td>\n",
-       "      <td>A</td>\n",
        "      <td>1</td>\n",
+       "      <td>0.993</td>\n",
+       "      <td>B</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>2</td>\n",
-       "      <td>0.998</td>\n",
+       "      <td>0.986</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>24</th>\n",
        "      <td>1</td>\n",
-       "      <td>1.000</td>\n",
-       "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0.941</td>\n",
+       "      <td>B</td>\n",
+       "      <td>1</td>\n",
        "      <td>A</td>\n",
        "      <td>2</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.886</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>25</th>\n",
        "      <td>2</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.992</td>\n",
        "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>2</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.984</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>26</th>\n",
+       "      <td>2</td>\n",
+       "      <td>0.999</td>\n",
+       "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.993</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>2</td>\n",
-       "      <td>0.986</td>\n",
+       "      <td>0.998</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>27</th>\n",
        "      <td>2</td>\n",
-       "      <td>0.998</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
+       "      <td>1.000</td>\n",
        "      <td>A</td>\n",
        "      <td>2</td>\n",
-       "      <td>0.995</td>\n",
+       "      <td>A</td>\n",
+       "      <td>2</td>\n",
+       "      <td>1.000</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>28</th>\n",
-       "      <td>1</td>\n",
-       "      <td>0.941</td>\n",
+       "      <td>2</td>\n",
+       "      <td>0.998</td>\n",
        "      <td>B</td>\n",
-       "      <td>1</td>\n",
+       "      <td>0</td>\n",
        "      <td>A</td>\n",
        "      <td>2</td>\n",
-       "      <td>0.886</td>\n",
+       "      <td>0.995</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>29</th>\n",
@@ -569,83 +548,83 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>31</th>\n",
-       "      <td>2</td>\n",
-       "      <td>0.992</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.289</td>\n",
        "      <td>A</td>\n",
-       "      <td>0</td>\n",
+       "      <td>1</td>\n",
        "      <td>B</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.984</td>\n",
+       "      <td>0.084</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>32</th>\n",
        "      <td>1</td>\n",
-       "      <td>-0.289</td>\n",
+       "      <td>0.993</td>\n",
        "      <td>A</td>\n",
-       "      <td>1</td>\n",
+       "      <td>2</td>\n",
        "      <td>B</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.084</td>\n",
+       "      <td>0.986</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>33</th>\n",
-       "      <td>2</td>\n",
-       "      <td>0.966</td>\n",
-       "      <td>A</td>\n",
        "      <td>1</td>\n",
+       "      <td>1.000</td>\n",
        "      <td>B</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.933</td>\n",
+       "      <td>B</td>\n",
+       "      <td>0</td>\n",
+       "      <td>1.000</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>34</th>\n",
        "      <td>1</td>\n",
-       "      <td>0.993</td>\n",
-       "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>-0.088</td>\n",
+       "      <td>B</td>\n",
+       "      <td>1</td>\n",
        "      <td>B</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.986</td>\n",
+       "      <td>0.008</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>35</th>\n",
        "      <td>2</td>\n",
-       "      <td>0.998</td>\n",
+       "      <td>0.992</td>\n",
        "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0</td>\n",
        "      <td>B</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.995</td>\n",
+       "      <td>0.984</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>36</th>\n",
+       "      <td>2</td>\n",
+       "      <td>0.966</td>\n",
+       "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>1.000</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
        "      <td>B</td>\n",
        "      <td>0</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.933</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>37</th>\n",
        "      <td>2</td>\n",
-       "      <td>1.000</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
+       "      <td>0.998</td>\n",
+       "      <td>A</td>\n",
+       "      <td>2</td>\n",
        "      <td>B</td>\n",
        "      <td>0</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.995</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>38</th>\n",
-       "      <td>1</td>\n",
-       "      <td>-0.088</td>\n",
+       "      <td>2</td>\n",
+       "      <td>1.000</td>\n",
        "      <td>B</td>\n",
-       "      <td>1</td>\n",
+       "      <td>0</td>\n",
        "      <td>B</td>\n",
        "      <td>0</td>\n",
-       "      <td>0.008</td>\n",
+       "      <td>1.000</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>39</th>\n",
@@ -669,80 +648,80 @@
        "    </tr>\n",
        "    <tr>\n",
        "      <th>41</th>\n",
-       "      <td>2</td>\n",
-       "      <td>0.988</td>\n",
+       "      <td>1</td>\n",
+       "      <td>0.998</td>\n",
        "      <td>A</td>\n",
-       "      <td>0</td>\n",
+       "      <td>1</td>\n",
        "      <td>B</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.976</td>\n",
+       "      <td>0.996</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>42</th>\n",
        "      <td>1</td>\n",
-       "      <td>0.998</td>\n",
+       "      <td>0.941</td>\n",
        "      <td>A</td>\n",
-       "      <td>1</td>\n",
+       "      <td>2</td>\n",
        "      <td>B</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.996</td>\n",
+       "      <td>0.886</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>43</th>\n",
-       "      <td>2</td>\n",
-       "      <td>0.991</td>\n",
-       "      <td>A</td>\n",
        "      <td>1</td>\n",
+       "      <td>-0.088</td>\n",
+       "      <td>B</td>\n",
+       "      <td>0</td>\n",
        "      <td>B</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.981</td>\n",
+       "      <td>0.008</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>44</th>\n",
        "      <td>1</td>\n",
-       "      <td>0.941</td>\n",
-       "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>1.000</td>\n",
        "      <td>B</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.886</td>\n",
+       "      <td>B</td>\n",
+       "      <td>1</td>\n",
+       "      <td>1.000</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>45</th>\n",
        "      <td>2</td>\n",
-       "      <td>0.996</td>\n",
+       "      <td>0.988</td>\n",
        "      <td>A</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0</td>\n",
        "      <td>B</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.993</td>\n",
+       "      <td>0.976</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>46</th>\n",
+       "      <td>2</td>\n",
+       "      <td>0.991</td>\n",
+       "      <td>A</td>\n",
        "      <td>1</td>\n",
-       "      <td>-0.088</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
        "      <td>B</td>\n",
        "      <td>1</td>\n",
-       "      <td>0.008</td>\n",
+       "      <td>0.981</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>47</th>\n",
        "      <td>2</td>\n",
-       "      <td>1.000</td>\n",
-       "      <td>B</td>\n",
-       "      <td>0</td>\n",
+       "      <td>0.996</td>\n",
+       "      <td>A</td>\n",
+       "      <td>2</td>\n",
        "      <td>B</td>\n",
        "      <td>1</td>\n",
-       "      <td>1.000</td>\n",
+       "      <td>0.993</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>48</th>\n",
-       "      <td>1</td>\n",
+       "      <td>2</td>\n",
        "      <td>1.000</td>\n",
        "      <td>B</td>\n",
-       "      <td>1</td>\n",
+       "      <td>0</td>\n",
        "      <td>B</td>\n",
        "      <td>1</td>\n",
        "      <td>1.000</td>\n",
@@ -764,54 +743,54 @@
       "text/plain": [
        "   epitope  correlation library_1  replicate_1 library_2  replicate_2     r2\n",
        "0        1        1.000         A            0         A            0  1.000\n",
-       "1        2        1.000         A            0         A            0  1.000\n",
-       "2        1        0.877         A            1         A            0  0.770\n",
-       "3        2        1.000         A            1         A            0  0.999\n",
-       "4        1        0.997         A            2         A            0  0.994\n",
-       "5        2        0.992         A            2         A            0  0.984\n",
-       "6        1        0.999         B            0         A            0  0.998\n",
-       "7        2        0.992         B            0         A            0  0.984\n",
-       "8        1        0.893         B            1         A            0  0.798\n",
+       "1        1        0.877         A            1         A            0  0.770\n",
+       "2        1        0.997         A            2         A            0  0.994\n",
+       "3        1        0.999         B            0         A            0  0.998\n",
+       "4        1        0.893         B            1         A            0  0.798\n",
+       "5        2        1.000         A            0         A            0  1.000\n",
+       "6        2        1.000         A            1         A            0  0.999\n",
+       "7        2        0.992         A            2         A            0  0.984\n",
+       "8        2        0.992         B            0         A            0  0.984\n",
        "9        2        0.988         B            1         A            0  0.976\n",
        "10       1        0.877         A            0         A            1  0.770\n",
-       "11       2        1.000         A            0         A            1  0.999\n",
-       "12       1        1.000         A            1         A            1  1.000\n",
-       "13       2        1.000         A            1         A            1  1.000\n",
-       "14       1        0.929         A            2         A            1  0.863\n",
-       "15       2        0.999         A            2         A            1  0.998\n",
-       "16       1       -0.289         B            0         A            1  0.084\n",
-       "17       2        0.966         B            0         A            1  0.933\n",
-       "18       1        0.998         B            1         A            1  0.996\n",
+       "11       1        1.000         A            1         A            1  1.000\n",
+       "12       1        0.929         A            2         A            1  0.863\n",
+       "13       1       -0.289         B            0         A            1  0.084\n",
+       "14       1        0.998         B            1         A            1  0.996\n",
+       "15       2        1.000         A            0         A            1  0.999\n",
+       "16       2        1.000         A            1         A            1  1.000\n",
+       "17       2        0.999         A            2         A            1  0.998\n",
+       "18       2        0.966         B            0         A            1  0.933\n",
        "19       2        0.991         B            1         A            1  0.981\n",
        "20       1        0.997         A            0         A            2  0.994\n",
-       "21       2        0.992         A            0         A            2  0.984\n",
-       "22       1        0.929         A            1         A            2  0.863\n",
-       "23       2        0.999         A            1         A            2  0.998\n",
-       "24       1        1.000         A            2         A            2  1.000\n",
-       "25       2        1.000         A            2         A            2  1.000\n",
-       "26       1        0.993         B            0         A            2  0.986\n",
-       "27       2        0.998         B            0         A            2  0.995\n",
-       "28       1        0.941         B            1         A            2  0.886\n",
+       "21       1        0.929         A            1         A            2  0.863\n",
+       "22       1        1.000         A            2         A            2  1.000\n",
+       "23       1        0.993         B            0         A            2  0.986\n",
+       "24       1        0.941         B            1         A            2  0.886\n",
+       "25       2        0.992         A            0         A            2  0.984\n",
+       "26       2        0.999         A            1         A            2  0.998\n",
+       "27       2        1.000         A            2         A            2  1.000\n",
+       "28       2        0.998         B            0         A            2  0.995\n",
        "29       2        0.996         B            1         A            2  0.993\n",
        "30       1        0.999         A            0         B            0  0.998\n",
-       "31       2        0.992         A            0         B            0  0.984\n",
-       "32       1       -0.289         A            1         B            0  0.084\n",
-       "33       2        0.966         A            1         B            0  0.933\n",
-       "34       1        0.993         A            2         B            0  0.986\n",
-       "35       2        0.998         A            2         B            0  0.995\n",
-       "36       1        1.000         B            0         B            0  1.000\n",
-       "37       2        1.000         B            0         B            0  1.000\n",
-       "38       1       -0.088         B            1         B            0  0.008\n",
+       "31       1       -0.289         A            1         B            0  0.084\n",
+       "32       1        0.993         A            2         B            0  0.986\n",
+       "33       1        1.000         B            0         B            0  1.000\n",
+       "34       1       -0.088         B            1         B            0  0.008\n",
+       "35       2        0.992         A            0         B            0  0.984\n",
+       "36       2        0.966         A            1         B            0  0.933\n",
+       "37       2        0.998         A            2         B            0  0.995\n",
+       "38       2        1.000         B            0         B            0  1.000\n",
        "39       2        1.000         B            1         B            0  1.000\n",
        "40       1        0.893         A            0         B            1  0.798\n",
-       "41       2        0.988         A            0         B            1  0.976\n",
-       "42       1        0.998         A            1         B            1  0.996\n",
-       "43       2        0.991         A            1         B            1  0.981\n",
-       "44       1        0.941         A            2         B            1  0.886\n",
-       "45       2        0.996         A            2         B            1  0.993\n",
-       "46       1       -0.088         B            0         B            1  0.008\n",
-       "47       2        1.000         B            0         B            1  1.000\n",
-       "48       1        1.000         B            1         B            1  1.000\n",
+       "41       1        0.998         A            1         B            1  0.996\n",
+       "42       1        0.941         A            2         B            1  0.886\n",
+       "43       1       -0.088         B            0         B            1  0.008\n",
+       "44       1        1.000         B            1         B            1  1.000\n",
+       "45       2        0.988         A            0         B            1  0.976\n",
+       "46       2        0.991         A            1         B            1  0.981\n",
+       "47       2        0.996         A            2         B            1  0.993\n",
+       "48       2        1.000         B            0         B            1  1.000\n",
        "49       2        1.000         B            1         B            1  1.000"
       ]
      },
@@ -847,13 +826,6 @@
    "execution_count": 4,
    "id": "fa1cdd44-0748-4a57-b56d-1d0cfc6ba073",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:14.822592Z",
-     "iopub.status.busy": "2023-07-19T19:40:14.822361Z",
-     "iopub.status.idle": "2023-07-19T19:40:14.992389Z",
-     "shell.execute_reply": "2023-07-19T19:40:14.991187Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:14.822572Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -862,28 +834,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-f2d873547c6f44938345a5b41a2799c7.vega-embed {\n",
+       "  #altair-viz-f820b11fb3c04122bb7635ae1404472e.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-f2d873547c6f44938345a5b41a2799c7.vega-embed details,\n",
-       "  #altair-viz-f2d873547c6f44938345a5b41a2799c7.vega-embed details summary {\n",
+       "  #altair-viz-f820b11fb3c04122bb7635ae1404472e.vega-embed details,\n",
+       "  #altair-viz-f820b11fb3c04122bb7635ae1404472e.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-f2d873547c6f44938345a5b41a2799c7\"></div>\n",
+       "<div id=\"altair-viz-f820b11fb3c04122bb7635ae1404472e\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-f2d873547c6f44938345a5b41a2799c7\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-f2d873547c6f44938345a5b41a2799c7\");\n",
+       "    if (outputDiv.id !== \"altair-viz-f820b11fb3c04122bb7635ae1404472e\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-f820b11fb3c04122bb7635ae1404472e\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -919,12 +891,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"labelLimit\": 500}}, \"data\": {\"name\": \"data-f28ad4c00b1c74baea882b1e907bb7ee\"}, \"mark\": {\"type\": \"rect\", \"stroke\": \"black\"}, \"encoding\": {\"color\": {\"field\": \"r2\", \"scale\": {\"domain\": [0, 1], \"scheme\": \"yellowgreenblue\"}, \"type\": \"quantitative\"}, \"facet\": {\"columns\": 3, \"field\": \"epitope\", \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"r\", \"format\": \".3f\", \"type\": \"quantitative\"}, {\"field\": \"r2\", \"format\": \".3f\", \"type\": \"quantitative\"}, {\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"library_1\", \"type\": \"nominal\"}, {\"field\": \"replicate_1\", \"type\": \"quantitative\"}, {\"field\": \"library_2\", \"type\": \"nominal\"}, {\"field\": \"replicate_2\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_label_1\", \"title\": null, \"type\": \"nominal\"}, \"y\": {\"field\": \"_label_2\", \"title\": null, \"type\": \"nominal\"}}, \"height\": {\"step\": 15}, \"width\": {\"step\": 15}, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.8.0.json\", \"datasets\": {\"data-f28ad4c00b1c74baea882b1e907bb7ee\": [{\"r\": 1.0, \"r2\": 1.0, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-0\", \"_label_2\": \"A-0\"}, {\"r\": 1.0, \"r2\": 1.0, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-0\", \"_label_2\": \"A-0\"}, {\"r\": 0.8773798123199854, \"r2\": 0.7697953350666528, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-1\", \"_label_2\": \"A-0\"}, {\"r\": 0.9996962573276795, \"r2\": 0.99939260691497, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-1\", \"_label_2\": \"A-0\"}, {\"r\": 0.9971295415789166, \"r2\": 0.9942673226893805, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 2, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-2\", \"_label_2\": \"A-0\"}, {\"r\": 0.9921010175738242, \"r2\": 0.9842644290710174, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 2, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-2\", \"_label_2\": \"A-0\"}, {\"r\": 0.9991858761797873, \"r2\": 0.9983724151571691, \"epitope\": \"1\", \"library_1\": \"B\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"B-0\", \"_label_2\": \"A-0\"}, {\"r\": 0.9917580348440374, \"r2\": 0.9835839996777068, \"epitope\": \"2\", \"library_1\": \"B\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"B-0\", \"_label_2\": \"A-0\"}, {\"r\": 0.8934312791152936, \"r2\": 0.7982194505015897, \"epitope\": \"1\", \"library_1\": \"B\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"B-1\", \"_label_2\": \"A-0\"}, {\"r\": 0.9877468639344096, \"r2\": 0.975643867212261, \"epitope\": \"2\", \"library_1\": \"B\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"B-1\", \"_label_2\": \"A-0\"}, {\"r\": 0.8773798123199854, \"r2\": 0.7697953350666528, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"A-0\", \"_label_2\": \"A-1\"}, {\"r\": 0.9996962573276795, \"r2\": 0.99939260691497, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"A-0\", \"_label_2\": \"A-1\"}, {\"r\": 1.0, \"r2\": 1.0, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"A-1\", \"_label_2\": \"A-1\"}, {\"r\": 1.0, \"r2\": 1.0, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"A-1\", \"_label_2\": \"A-1\"}, {\"r\": 0.92919195563458, \"r2\": 0.8633976904160153, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 2, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"A-2\", \"_label_2\": \"A-1\"}, {\"r\": 0.998937533707095, \"r2\": 0.9978761962488136, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 2, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"A-2\", \"_label_2\": \"A-1\"}, {\"r\": -0.28905012331204355, \"r2\": 0.08354997378670759, \"epitope\": \"1\", \"library_1\": \"B\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"B-0\", \"_label_2\": \"A-1\"}, {\"r\": 0.9660388215724064, \"r2\": 0.9332310047850036, \"epitope\": \"2\", \"library_1\": \"B\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"B-0\", \"_label_2\": \"A-1\"}, {\"r\": 0.997789750783417, \"r2\": 0.9955843867684334, \"epitope\": \"1\", \"library_1\": \"B\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"B-1\", \"_label_2\": \"A-1\"}, {\"r\": 0.9906131641014112, \"r2\": 0.9813144408910094, \"epitope\": \"2\", \"library_1\": \"B\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 1, \"_label_1\": \"B-1\", \"_label_2\": \"A-1\"}, {\"r\": 0.9971295415789166, \"r2\": 0.9942673226893805, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 2, \"_label_1\": \"A-0\", \"_label_2\": \"A-2\"}, {\"r\": 0.9921010175738242, \"r2\": 0.9842644290710174, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 2, \"_label_1\": \"A-0\", \"_label_2\": \"A-2\"}, {\"r\": 0.92919195563458, \"r2\": 0.8633976904160153, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 1, \"library_2\": \"A\", \"replicate_2\": 2, \"_label_1\": \"A-1\", \"_label_2\": \"A-2\"}, {\"r\": 0.998937533707095, \"r2\": 0.9978761962488136, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 1, 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-       "  #altair-viz-c91c3188b5a5474187bb0f64c4a3377c.vega-embed details,\n",
-       "  #altair-viz-c91c3188b5a5474187bb0f64c4a3377c.vega-embed details summary {\n",
+       "  #altair-viz-72106f11304d4950aa7282a7d3958a68.vega-embed details,\n",
+       "  #altair-viz-72106f11304d4950aa7282a7d3958a68.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-c91c3188b5a5474187bb0f64c4a3377c\"></div>\n",
+       "<div id=\"altair-viz-72106f11304d4950aa7282a7d3958a68\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-c91c3188b5a5474187bb0f64c4a3377c\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-c91c3188b5a5474187bb0f64c4a3377c\");\n",
+       "    if (outputDiv.id !== \"altair-viz-72106f11304d4950aa7282a7d3958a68\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-72106f11304d4950aa7282a7d3958a68\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -1243,12 +1194,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false}}, \"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 18.75}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": null, \"scale\": {\"domain\": [\"1\", \"2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"activity_median\", \"title\": \"activity_median\", \"type\": \"quantitative\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}, {\"mark\": {\"type\": \"rule\", \"size\": 2}, \"encoding\": {\"color\": {\"value\": \"black\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_lower\", \"type\": \"quantitative\"}, \"x2\": {\"field\": \"_upper\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}], \"data\": {\"name\": \"data-ffe21e155a2a18b3ba0f003b58f87b0d\"}, \"height\": {\"step\": 25}, \"width\": 110, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.8.0.json\", \"datasets\": {\"data-ffe21e155a2a18b3ba0f003b58f87b0d\": [{\"epitope\": \"1\", \"activity_mean\": 2.583931630472031, \"activity_median\": 2.5488135039273248, \"activity_std\": 0.22295709390357102, \"_lower\": 2.3258564100237535, \"_upper\": 2.771770597830896}, {\"epitope\": \"2\", \"activity_mean\": 1.543364032687259, \"activity_median\": 1.7081478226181048, \"activity_std\": 0.2982236946687655, \"_lower\": 1.4099241279493393, \"_upper\": 2.0063715172868704}]}}, {\"mode\": \"vega-lite\"});\n",
+       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false}}, \"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 18.75}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": null, \"scale\": {\"domain\": [\"1\", \"2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"activity_median\", \"title\": \"activity_median\", \"type\": \"quantitative\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}, {\"mark\": {\"type\": \"rule\", \"size\": 2}, \"encoding\": {\"color\": {\"value\": \"black\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_lower\", \"type\": \"quantitative\"}, \"x2\": {\"field\": \"_upper\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}], \"data\": {\"name\": \"data-ffe21e155a2a18b3ba0f003b58f87b0d\"}, \"height\": {\"step\": 25}, \"width\": 110, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.16.3.json\", \"datasets\": {\"data-ffe21e155a2a18b3ba0f003b58f87b0d\": [{\"epitope\": \"1\", \"activity_mean\": 2.583931630472031, \"activity_median\": 2.5488135039273248, \"activity_std\": 0.22295709390357102, \"_lower\": 2.3258564100237535, \"_upper\": 2.771770597830896}, {\"epitope\": \"2\", \"activity_mean\": 1.543364032687259, \"activity_median\": 1.7081478226181048, \"activity_std\": 0.2982236946687655, \"_lower\": 1.4099241279493393, \"_upper\": 2.0063715172868704}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -1278,43 +1229,35 @@
    "cell_type": "code",
    "execution_count": 8,
    "id": "5e784d25-67cc-49e7-be35-3689e4c2128d",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:15.128820Z",
-     "iopub.status.busy": "2023-07-19T19:40:15.128502Z",
-     "iopub.status.idle": "2023-07-19T19:40:15.209162Z",
-     "shell.execute_reply": "2023-07-19T19:40:15.208389Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:15.128799Z"
-    }
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-df6f46e9dd634495b32a4d9a2d6be910.vega-embed {\n",
+       "  #altair-viz-6d6f703ab8414bcb9bd38206715bf1cf.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-df6f46e9dd634495b32a4d9a2d6be910.vega-embed details,\n",
-       "  #altair-viz-df6f46e9dd634495b32a4d9a2d6be910.vega-embed details summary {\n",
+       "  #altair-viz-6d6f703ab8414bcb9bd38206715bf1cf.vega-embed details,\n",
+       "  #altair-viz-6d6f703ab8414bcb9bd38206715bf1cf.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-df6f46e9dd634495b32a4d9a2d6be910\"></div>\n",
+       "<div id=\"altair-viz-6d6f703ab8414bcb9bd38206715bf1cf\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-df6f46e9dd634495b32a4d9a2d6be910\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-df6f46e9dd634495b32a4d9a2d6be910\");\n",
+       "    if (outputDiv.id !== \"altair-viz-6d6f703ab8414bcb9bd38206715bf1cf\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-6d6f703ab8414bcb9bd38206715bf1cf\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -1350,12 +1293,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false}}, \"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 18.75}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": null, \"scale\": {\"domain\": [\"1\", \"2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"activity_mean\", \"title\": \"activity_mean\", \"type\": \"quantitative\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}, {\"mark\": {\"type\": \"rule\", \"size\": 2}, \"encoding\": {\"color\": {\"value\": \"black\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_lower\", \"type\": \"quantitative\"}, \"x2\": {\"field\": \"_upper\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}], \"data\": {\"name\": \"data-e24935b20356632687c18b9f2bdebe0f\"}, \"height\": {\"step\": 25}, \"width\": 110, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.8.0.json\", \"datasets\": {\"data-e24935b20356632687c18b9f2bdebe0f\": [{\"epitope\": \"1\", \"activity_mean\": 2.583931630472031, \"activity_median\": 2.5488135039273248, \"activity_std\": 0.22295709390357102, \"_lower\": 2.3609745365684596, \"_upper\": 2.806888724375602}, {\"epitope\": \"2\", \"activity_mean\": 1.543364032687259, \"activity_median\": 1.7081478226181048, \"activity_std\": 0.2982236946687655, \"_lower\": 1.2451403380184936, \"_upper\": 1.8415877273560246}]}}, {\"mode\": \"vega-lite\"});\n",
+       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false}}, \"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 18.75}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": null, \"scale\": {\"domain\": [\"1\", \"2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"activity_mean\", \"title\": \"activity_mean\", \"type\": \"quantitative\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}, {\"mark\": {\"type\": \"rule\", \"size\": 2}, \"encoding\": {\"color\": {\"value\": \"black\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_lower\", \"type\": \"quantitative\"}, \"x2\": {\"field\": \"_upper\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}], \"data\": {\"name\": \"data-e24935b20356632687c18b9f2bdebe0f\"}, \"height\": {\"step\": 25}, \"width\": 110, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.16.3.json\", \"datasets\": {\"data-e24935b20356632687c18b9f2bdebe0f\": [{\"epitope\": \"1\", \"activity_mean\": 2.583931630472031, \"activity_median\": 2.5488135039273248, \"activity_std\": 0.22295709390357102, \"_lower\": 2.3609745365684596, \"_upper\": 2.806888724375602}, {\"epitope\": \"2\", \"activity_mean\": 1.543364032687259, \"activity_median\": 1.7081478226181048, \"activity_std\": 0.2982236946687655, \"_lower\": 1.2451403380184936, \"_upper\": 1.8415877273560246}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -1386,13 +1329,6 @@
    "execution_count": 9,
    "id": "4520c763-f8da-45cc-9987-bcbb2214f85e",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:15.210452Z",
-     "iopub.status.busy": "2023-07-19T19:40:15.210162Z",
-     "iopub.status.idle": "2023-07-19T19:40:15.371701Z",
-     "shell.execute_reply": "2023-07-19T19:40:15.371100Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:15.210434Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -1930,13 +1866,6 @@
    "execution_count": 10,
    "id": "0e88ba97-d25c-4d5a-a6f2-469bd90d39d7",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:15.373077Z",
-     "iopub.status.busy": "2023-07-19T19:40:15.372746Z",
-     "iopub.status.idle": "2023-07-19T19:40:15.430205Z",
-     "shell.execute_reply": "2023-07-19T19:40:15.429502Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:15.373058Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -2159,13 +2088,6 @@
    "execution_count": 11,
    "id": "52b6b660-a2fc-461d-bf2f-d4aebb624314",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:15.431276Z",
-     "iopub.status.busy": "2023-07-19T19:40:15.431010Z",
-     "iopub.status.idle": "2023-07-19T19:40:16.700983Z",
-     "shell.execute_reply": "2023-07-19T19:40:16.700405Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:15.431258Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -2174,28 +2096,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-e1258ed41f7f41fa86947cc4aa509d7e.vega-embed {\n",
+       "  #altair-viz-0dc7d7638cbd4103a88c30e19371c75d.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-e1258ed41f7f41fa86947cc4aa509d7e.vega-embed details,\n",
-       "  #altair-viz-e1258ed41f7f41fa86947cc4aa509d7e.vega-embed details summary {\n",
+       "  #altair-viz-0dc7d7638cbd4103a88c30e19371c75d.vega-embed details,\n",
+       "  #altair-viz-0dc7d7638cbd4103a88c30e19371c75d.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-e1258ed41f7f41fa86947cc4aa509d7e\"></div>\n",
+       "<div id=\"altair-viz-0dc7d7638cbd4103a88c30e19371c75d\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-e1258ed41f7f41fa86947cc4aa509d7e\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-e1258ed41f7f41fa86947cc4aa509d7e\");\n",
+       "    if (outputDiv.id !== \"altair-viz-0dc7d7638cbd4103a88c30e19371c75d\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-0dc7d7638cbd4103a88c30e19371c75d\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -2231,12 +2153,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
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{\"site\": \"1\", \"mutant\": \"C\", \"escape\": 0.3006146806669343, \"epitope\": \"epitope 2\", \"A 0\": 0.4375872112626925, \"A 1\": 0.3965807272960261, \"A 2\": 0.2046486340378425, \"B 0\": null, \"B 1\": 0.14146417361702357, \"n_models\": 4.0, \"escape_std\": 0.14420628347773592}, {\"site\": \"2\", \"mutant\": \"A\", \"escape\": 0.29965467367452314, \"epitope\": \"epitope 2\", \"A 0\": 0.9636627605010293, \"A 1\": null, \"A 2\": 0.29965467367452314, \"B 0\": 0.20724287813818676, \"B 1\": null, \"n_models\": 3.0, \"escape_std\": 0.4126373948474744}, {\"site\": \"4\", \"mutant\": \"K\", \"escape\": 3.132963104392461, \"epitope\": \"epitope 2\", \"A 0\": 3.2917250380826646, \"A 1\": 3.346310916686017, \"A 2\": 3.121133832769295, \"B 0\": 2.9408098436506362, \"B 1\": 3.132963104392461, \"n_models\": 5.0, \"escape_std\": 0.15979056283813148}, {\"site\": \"4\", \"mutant\": \"L\", \"escape\": 2.0245481595728716, \"epitope\": \"epitope 2\", \"A 0\": null, \"A 1\": 2.0245481595728716, \"A 2\": null, \"B 0\": 1.956833224394711, \"B 1\": 2.07235649126018, \"n_models\": 3.0, \"escape_std\": 0.05804678316119469}, {\"site\": \"4\", \"mutant\": \"Q\", \"escape\": 3.7295772137298258, \"epitope\": \"epitope 2\", \"A 0\": 3.571036058197887, \"A 1\": 3.7295772137298258, \"A 2\": 3.6844398656469153, \"B 0\": 3.7784872826479754, \"B 1\": 4.104131938247697, \"n_models\": 5.0, \"escape_std\": 0.2001217829541086}, {\"site\": \"1\", \"mutant\": \"M\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"2\", \"mutant\": \"G\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"4\", \"mutant\": \"A\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"1\", \"mutant\": \"M\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"2\", \"mutant\": \"G\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"4\", \"mutant\": \"A\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}], \"data-a7d600054b448517d77aab4449a3c18a\": [{\"site\": \"1\", \"wildtype\": \"M\", \"_stat_site_order\": 0}, {\"site\": \"2\", \"wildtype\": \"G\", \"_stat_site_order\": 1}, {\"site\": \"4\", \"wildtype\": \"A\", \"_stat_site_order\": 2}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -2267,13 +2189,6 @@
    "execution_count": 12,
    "id": "957a1c96-80e2-4880-8c34-0a31eb8166a7",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:16.701913Z",
-     "iopub.status.busy": "2023-07-19T19:40:16.701722Z",
-     "iopub.status.idle": "2023-07-19T19:40:16.774220Z",
-     "shell.execute_reply": "2023-07-19T19:40:16.773536Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:16.701896Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -2720,13 +2635,6 @@
    "execution_count": 13,
    "id": "a8ba5f75-a935-4342-a867-931691e54e47",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:16.775317Z",
-     "iopub.status.busy": "2023-07-19T19:40:16.775019Z",
-     "iopub.status.idle": "2023-07-19T19:40:16.862604Z",
-     "shell.execute_reply": "2023-07-19T19:40:16.861893Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:16.775299Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -3238,13 +3146,6 @@
    "execution_count": 14,
    "id": "688be46d-8d22-45b8-9f4a-3c3df3bc2f05",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:16.863702Z",
-     "iopub.status.busy": "2023-07-19T19:40:16.863410Z",
-     "iopub.status.idle": "2023-07-19T19:40:18.270304Z",
-     "shell.execute_reply": "2023-07-19T19:40:18.269314Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:16.863684Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -3253,28 +3154,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-f04d0bc493074a22bffbf0a0c834c3e7.vega-embed {\n",
+       "  #altair-viz-2c6d5b97d08043a79b13a2d31efd9aa8.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-f04d0bc493074a22bffbf0a0c834c3e7.vega-embed details,\n",
-       "  #altair-viz-f04d0bc493074a22bffbf0a0c834c3e7.vega-embed details summary {\n",
+       "  #altair-viz-2c6d5b97d08043a79b13a2d31efd9aa8.vega-embed details,\n",
+       "  #altair-viz-2c6d5b97d08043a79b13a2d31efd9aa8.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-f04d0bc493074a22bffbf0a0c834c3e7\"></div>\n",
+       "<div id=\"altair-viz-2c6d5b97d08043a79b13a2d31efd9aa8\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-f04d0bc493074a22bffbf0a0c834c3e7\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-f04d0bc493074a22bffbf0a0c834c3e7\");\n",
+       "    if (outputDiv.id !== \"altair-viz-2c6d5b97d08043a79b13a2d31efd9aa8\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-2c6d5b97d08043a79b13a2d31efd9aa8\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -3310,12 +3211,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false, \"labelOverlap\": \"parity\"}, \"padding\": 10}, \"vconcat\": [{\"data\": {\"name\": \"data-42e7f5dbd0282babbfecc80c452dbb2f\"}, \"mark\": {\"type\": \"rect\"}, \"encoding\": {\"color\": {\"value\": \"gray\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"nominal\"}], \"x\": {\"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}}, \"height\": 11, \"name\": \"view_6\", \"title\": \"site zoom bar\", \"width\": 500}, {\"layer\": [{\"mark\": {\"type\": \"line\", \"opacity\": 0.7, \"size\": 1}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": {\"orient\": \"left\"}, \"scale\": {\"domain\": [\"epitope 1\", \"epitope 2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"nominal\"}, {\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"_stat_site_val\", \"format\": \".3g\", \"title\": \"site escape\", \"type\": \"quantitative\"}, {\"field\": \"wildtype\", \"type\": \"nominal\"}], \"x\": {\"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}, \"y\": {\"field\": \"_stat_site_val\", \"scale\": {\"zero\": true}, \"title\": \"site escape\", \"type\": \"quantitative\"}}, \"name\": \"view_5\", \"transform\": [{\"lookup\": \"site\", \"from\": {\"data\": {\"name\": \"data-a7d600054b448517d77aab4449a3c18a\"}, \"key\": \"site\", \"fields\": [\"wildtype\", \"_stat_site_order\"]}}, {\"calculate\": \"if(isFinite(datum['escape']),datum['escape'],NaN)\", \"as\": \"escape\"}, {\"calculate\": \"if(isFinite(datum['A 0']),datum['A 0'],NaN)\", \"as\": \"A 0\"}, {\"calculate\": \"if(isFinite(datum['A 1']),datum['A 1'],NaN)\", \"as\": \"A 1\"}, {\"calculate\": \"if(isFinite(datum['A 2']),datum['A 2'],NaN)\", \"as\": \"A 2\"}, {\"calculate\": \"if(isFinite(datum['B 0']),datum['B 0'],NaN)\", \"as\": \"B 0\"}, {\"calculate\": \"if(isFinite(datum['B 1']),datum['B 1'],NaN)\", \"as\": \"B 1\"}, {\"calculate\": \"if(isFinite(datum['n_models']),datum['n_models'],NaN)\", \"as\": \"n_models\"}, {\"calculate\": \"max(datum['escape'],floor_at_zero['floor'])\", \"as\": \"_stat\"}, {\"calculate\": \"false\", \"as\": \"_stat_hide\"}, {\"filter\": \"((datum['n_models'] >= (param_5['cutoff'] - 1e-06)) || (!isFinite(datum['n_models'])))\"}, {\"calculate\": \"if(datum['_stat_hide'],0.0,datum['_stat'])\", \"as\": \"_stat_not_hidden\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_hidden\", \"as\": \"_stat_site_max\"}], \"groupby\": [\"site\"]}, {\"filter\": \"((datum['_stat_site_max'] >= (param_6['cutoff'] - 1e-06)) || (!isFinite(datum['_stat_site_max'])))\"}, {\"calculate\": \"(datum.wildtype !== datum.mutant)\", \"as\": \"_stat_not_wildtype\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_wildtype\", \"as\": \"_stat_site_has_non_wildtype\"}], \"groupby\": [\"site\"]}, {\"filter\": \"datum['_stat_site_has_non_wildtype']\"}, {\"filter\": {\"param\": \"param_8\"}}, {\"filter\": \"((datum.wildtype !== datum.mutant) && (!datum['_stat_hide']))\"}, {\"aggregate\": [{\"op\": \"sum\", \"field\": \"_stat\", \"as\": \"_stat_sum\"}, {\"op\": \"mean\", \"field\": \"_stat\", \"as\": \"_stat_mean\"}, {\"op\": \"max\", \"field\": \"_stat\", \"as\": \"_stat_max\"}, {\"op\": \"min\", \"field\": \"_stat\", \"as\": \"_stat_min\"}], \"groupby\": [\"site\", \"wildtype\", \"_stat_site_order\", \"epitope\"]}, {\"fold\": [\"_stat_sum\", \"_stat_mean\", \"_stat_max\", \"_stat_min\"], \"as\": [\"_stat_site_stat\", \"_stat_site_val\"]}, {\"filter\": {\"param\": \"site_stat\"}}, {\"calculate\": \"true\", \"as\": \"_stat_show_line\"}, {\"filter\": {\"param\": \"param_7\"}}]}, {\"mark\": {\"type\": \"circle\", \"opacity\": 0.7}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": {\"orient\": \"left\"}, 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{\"calculate\": \"if(isFinite(datum['A 1']),datum['A 1'],NaN)\", \"as\": \"A 1\"}, {\"calculate\": \"if(isFinite(datum['A 2']),datum['A 2'],NaN)\", \"as\": \"A 2\"}, {\"calculate\": \"if(isFinite(datum['B 0']),datum['B 0'],NaN)\", \"as\": \"B 0\"}, {\"calculate\": \"if(isFinite(datum['B 1']),datum['B 1'],NaN)\", \"as\": \"B 1\"}, {\"calculate\": \"if(isFinite(datum['n_models']),datum['n_models'],NaN)\", \"as\": \"n_models\"}, {\"calculate\": \"max(datum['escape'],floor_at_zero['floor'])\", \"as\": \"_stat\"}, {\"calculate\": \"false\", \"as\": \"_stat_hide\"}, {\"filter\": \"((datum['n_models'] >= (param_5['cutoff'] - 1e-06)) || (!isFinite(datum['n_models'])))\"}, {\"calculate\": \"if(datum['_stat_hide'],0.0,datum['_stat'])\", \"as\": \"_stat_not_hidden\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_hidden\", \"as\": \"_stat_site_max\"}], \"groupby\": [\"site\"]}, {\"filter\": \"((datum['_stat_site_max'] >= (param_6['cutoff'] - 1e-06)) || (!isFinite(datum['_stat_site_max'])))\"}, {\"calculate\": \"(datum.wildtype !== datum.mutant)\", \"as\": \"_stat_not_wildtype\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_wildtype\", \"as\": \"_stat_site_has_non_wildtype\"}], \"groupby\": [\"site\"]}, {\"filter\": \"datum['_stat_site_has_non_wildtype']\"}, {\"filter\": {\"param\": \"param_8\"}}, {\"filter\": \"((datum.wildtype !== datum.mutant) && (!datum['_stat_hide']))\"}, {\"aggregate\": [{\"op\": \"sum\", \"field\": \"_stat\", \"as\": \"_stat_sum\"}, {\"op\": \"mean\", \"field\": \"_stat\", \"as\": \"_stat_mean\"}, {\"op\": \"max\", \"field\": \"_stat\", \"as\": \"_stat_max\"}, {\"op\": \"min\", \"field\": \"_stat\", \"as\": \"_stat_min\"}], \"groupby\": [\"site\", \"wildtype\", \"_stat_site_order\", \"epitope\"]}, {\"fold\": [\"_stat_sum\", \"_stat_mean\", \"_stat_max\", \"_stat_min\"], \"as\": [\"_stat_site_stat\", \"_stat_site_val\"]}, {\"filter\": {\"param\": \"site_stat\"}}]}], \"data\": {\"name\": 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{\"calculate\": \"if(isFinite(datum['A 0']),datum['A 0'],NaN)\", \"as\": \"A 0\"}, {\"calculate\": \"if(isFinite(datum['A 1']),datum['A 1'],NaN)\", \"as\": \"A 1\"}, {\"calculate\": \"if(isFinite(datum['A 2']),datum['A 2'],NaN)\", \"as\": \"A 2\"}, {\"calculate\": \"if(isFinite(datum['B 0']),datum['B 0'],NaN)\", \"as\": \"B 0\"}, {\"calculate\": \"if(isFinite(datum['B 1']),datum['B 1'],NaN)\", \"as\": \"B 1\"}, {\"calculate\": \"if(isFinite(datum['n_models']),datum['n_models'],NaN)\", \"as\": \"n_models\"}, {\"calculate\": \"max(datum['escape'],floor_at_zero['floor'])\", \"as\": \"_stat\"}, {\"calculate\": \"false\", \"as\": \"_stat_hide\"}, {\"filter\": \"((datum['n_models'] >= (param_5['cutoff'] - 1e-06)) || (!isFinite(datum['n_models'])))\"}, {\"calculate\": \"if(datum['_stat_hide'],0.0,datum['_stat'])\", \"as\": \"_stat_not_hidden\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_hidden\", \"as\": \"_stat_site_max\"}], \"groupby\": [\"site\"]}, {\"filter\": 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\"type\": \"quantitative\"}, \"stroke\": {\"value\": \"black\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"nominal\"}, {\"field\": \"wildtype\", \"type\": \"nominal\"}, {\"field\": \"mutant\", \"type\": \"nominal\"}, {\"field\": \"escape\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"A 0\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"A 1\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"A 2\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"B 0\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"B 1\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"n_models\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"escape_std\", \"format\": \".3g\", \"type\": \"quantitative\"}], \"x\": {\"axis\": {\"labels\": true, \"ticks\": true, \"title\": \"site\"}, \"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}, \"y\": {\"field\": \"mutant\", \"scale\": {\"domain\": [\"R\", \"K\", \"H\", \"D\", \"E\", \"Q\", \"N\", \"S\", \"T\", \"Y\", \"W\", \"F\", \"A\", \"I\", \"L\", \"M\", \"V\", \"G\", \"P\", \"C\"]}, \"sort\": [\"R\", \"K\", \"H\", \"D\", \"E\", \"Q\", \"N\", \"S\", \"T\", \"Y\", \"W\", \"F\", \"A\", \"I\", \"L\", \"M\", \"V\", \"G\", \"P\", \"C\"], \"title\": null, \"type\": \"nominal\"}}, \"title\": {\"text\": \"epitope 2\", \"anchor\": \"middle\", \"color\": \"#CC79A7\", \"orient\": \"left\"}, \"transform\": [{\"lookup\": \"site\", \"from\": {\"data\": {\"name\": \"data-a7d600054b448517d77aab4449a3c18a\"}, \"key\": \"site\", \"fields\": [\"wildtype\", \"_stat_site_order\"]}}, {\"calculate\": \"if(isFinite(datum['escape']),datum['escape'],NaN)\", \"as\": \"escape\"}, {\"calculate\": \"if(isFinite(datum['A 0']),datum['A 0'],NaN)\", \"as\": \"A 0\"}, {\"calculate\": \"if(isFinite(datum['A 1']),datum['A 1'],NaN)\", \"as\": \"A 1\"}, {\"calculate\": \"if(isFinite(datum['A 2']),datum['A 2'],NaN)\", \"as\": \"A 2\"}, {\"calculate\": \"if(isFinite(datum['B 0']),datum['B 0'],NaN)\", \"as\": \"B 0\"}, {\"calculate\": \"if(isFinite(datum['B 1']),datum['B 1'],NaN)\", \"as\": \"B 1\"}, {\"calculate\": \"if(isFinite(datum['n_models']),datum['n_models'],NaN)\", \"as\": \"n_models\"}, {\"calculate\": \"if(isFinite(datum['escape_std']),datum['escape_std'],NaN)\", \"as\": \"escape_std\"}, {\"calculate\": \"max(datum['escape'],floor_at_zero['floor'])\", \"as\": \"_stat\"}, {\"calculate\": \"false\", \"as\": \"_stat_hide\"}, {\"filter\": \"(((datum['n_models'] >= (param_6 - 1e-06)) || (!isFinite(datum['n_models']))) || datum['_stat_hide'])\"}, {\"filter\": \"(((datum['escape_std'] <= (param_7 + 1e-06)) || (!isFinite(datum['escape_std']))) || datum['_stat_hide'])\"}, {\"calculate\": \"if(datum['_stat_hide'],0.0,datum['_stat'])\", \"as\": \"_stat_not_hidden\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_hidden\", \"as\": \"_stat_site_max\"}], \"groupby\": [\"site\"]}, {\"filter\": \"(((datum['_stat_site_max'] >= (param_8 - 1e-06)) || (!isFinite(datum['_stat_site_max']))) || datum['_stat_hide'])\"}, {\"calculate\": \"(datum.wildtype !== datum.mutant)\", \"as\": \"_stat_not_wildtype\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_wildtype\", \"as\": \"_stat_site_has_non_wildtype\"}], \"groupby\": [\"site\"]}, {\"filter\": \"datum['_stat_site_has_non_wildtype']\"}, {\"filter\": {\"param\": \"param_10\"}}, {\"filter\": \"(datum['epitope'] === 'epitope 2')\"}, {\"filter\": \"(!datum['_stat_hide'])\"}]}, {\"mark\": {\"type\": \"text\", \"color\": \"black\", \"text\": \"x\"}, \"encoding\": {\"x\": {\"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}, \"y\": {\"field\": \"mutant\", \"scale\": {\"domain\": [\"R\", \"K\", \"H\", \"D\", \"E\", \"Q\", \"N\", \"S\", \"T\", \"Y\", \"W\", \"F\", \"A\", \"I\", \"L\", \"M\", \"V\", \"G\", \"P\", \"C\"]}, \"sort\": [\"R\", \"K\", \"H\", \"D\", \"E\", \"Q\", \"N\", \"S\", \"T\", \"Y\", \"W\", \"F\", \"A\", \"I\", \"L\", \"M\", \"V\", \"G\", \"P\", \"C\"], \"title\": null, \"type\": \"nominal\"}}, \"transform\": [{\"lookup\": \"site\", \"from\": {\"data\": {\"name\": \"data-a7d600054b448517d77aab4449a3c18a\"}, \"key\": \"site\", \"fields\": [\"wildtype\", \"_stat_site_order\"]}}, {\"calculate\": \"if(isFinite(datum['escape']),datum['escape'],NaN)\", \"as\": \"escape\"}, {\"calculate\": \"if(isFinite(datum['A 0']),datum['A 0'],NaN)\", \"as\": \"A 0\"}, {\"calculate\": \"if(isFinite(datum['A 1']),datum['A 1'],NaN)\", \"as\": \"A 1\"}, {\"calculate\": \"if(isFinite(datum['A 2']),datum['A 2'],NaN)\", \"as\": \"A 2\"}, {\"calculate\": \"if(isFinite(datum['B 0']),datum['B 0'],NaN)\", \"as\": \"B 0\"}, {\"calculate\": \"if(isFinite(datum['B 1']),datum['B 1'],NaN)\", \"as\": \"B 1\"}, {\"calculate\": \"if(isFinite(datum['n_models']),datum['n_models'],NaN)\", \"as\": \"n_models\"}, {\"calculate\": \"if(isFinite(datum['escape_std']),datum['escape_std'],NaN)\", \"as\": \"escape_std\"}, {\"calculate\": \"max(datum['escape'],floor_at_zero['floor'])\", \"as\": \"_stat\"}, {\"calculate\": \"false\", \"as\": \"_stat_hide\"}, {\"filter\": \"(((datum['n_models'] >= (param_6 - 1e-06)) || (!isFinite(datum['n_models']))) || datum['_stat_hide'])\"}, {\"filter\": \"(((datum['escape_std'] <= (param_7 + 1e-06)) || (!isFinite(datum['escape_std']))) || datum['_stat_hide'])\"}, {\"calculate\": \"if(datum['_stat_hide'],0.0,datum['_stat'])\", \"as\": \"_stat_not_hidden\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_hidden\", \"as\": \"_stat_site_max\"}], \"groupby\": [\"site\"]}, {\"filter\": \"(((datum['_stat_site_max'] >= (param_8 - 1e-06)) || (!isFinite(datum['_stat_site_max']))) || datum['_stat_hide'])\"}, {\"calculate\": \"(datum.wildtype !== datum.mutant)\", \"as\": \"_stat_not_wildtype\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_wildtype\", \"as\": \"_stat_site_has_non_wildtype\"}], \"groupby\": [\"site\"]}, {\"filter\": \"datum['_stat_site_has_non_wildtype']\"}, {\"filter\": {\"param\": \"param_10\"}}, {\"filter\": \"(datum.wildtype === datum.mutant)\"}]}], \"height\": {\"step\": 11}, \"width\": {\"step\": 11}}], \"data\": {\"name\": \"data-b367b4916fe032dae7f5c728ade839ae\"}, \"resolve\": {\"scale\": {\"color\": \"independent\", \"x\": \"shared\"}}, \"spacing\": 10}], \"params\": [{\"name\": \"param_10\", \"select\": {\"type\": \"interval\", \"encodings\": [\"x\"], \"mark\": {\"stroke\": \"black\", \"strokeWidth\": 2}}, \"views\": [\"view_6\", \"view_5\", \"view_7\", \"view_8\"]}, {\"name\": \"site_stat\", \"select\": {\"type\": \"point\", \"fields\": [\"_stat_site_stat\"]}, \"bind\": {\"input\": \"radio\", \"options\": [\"_stat_sum\", \"_stat_mean\", \"_stat_max\", \"_stat_min\"], \"labels\": [\"sum\", \"mean\", \"max\", \"min\"], \"name\": \"site escape statistic\"}, \"value\": [{\"_stat_site_stat\": \"_stat_sum\"}], \"views\": [\"view_5\"]}, {\"name\": \"param_9\", \"select\": {\"type\": \"point\", \"fields\": [\"_stat_show_line\"]}, \"bind\": {\"input\": \"radio\", \"options\": [true, false], \"labels\": [\"yes\", \"no\"], \"name\": \"show line on site plot\"}, \"value\": [{\"_stat_show_line\": true}], \"views\": [\"view_5\"]}, {\"name\": \"floor_at_zero\", \"select\": {\"type\": \"point\", \"fields\": [\"floor\"]}, \"bind\": {\"input\": \"radio\", \"options\": [0, 0.029876210878566956], \"labels\": [\"yes\", \"no\"], \"name\": \"floor escape at zero\"}, \"value\": [{\"floor\": 0}], \"views\": [\"view_6\", \"view_5\", \"view_7\", \"view_8\"]}, {\"name\": \"param_6\", \"bind\": {\"input\": \"range\", \"max\": 5.0, \"min\": 3.0, \"name\": \"minimum n_models\"}, \"value\": 3}, {\"name\": \"param_7\", \"bind\": {\"input\": \"range\", \"max\": 0.4126373948474744, \"min\": 0.05804678316119469, \"name\": \"maximum escape_std\"}, \"value\": 0.4126373948474744}, {\"name\": \"param_8\", \"bind\": {\"input\": \"range\", \"max\": 3.7295772137298258, \"min\": 0.029876210878566956, \"name\": \"minimum max of escape at site\"}, \"value\": 0.029876210878566956}], \"resolve\": {\"scale\": {\"color\": \"independent\"}}, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.16.3.json\", \"datasets\": {\"data-42e7f5dbd0282babbfecc80c452dbb2f\": [{\"site\": \"1\", \"_stat_site_order\": 0}, {\"site\": \"2\", \"_stat_site_order\": 1}, {\"site\": \"4\", \"_stat_site_order\": 2}], \"data-b367b4916fe032dae7f5c728ade839ae\": [{\"site\": \"1\", \"mutant\": \"C\", \"escape\": 2.4639455131088055, \"epitope\": \"epitope 1\", \"A 0\": 2.6458941130666562, \"A 1\": 2.236088976951976, \"A 2\": 2.3303348210038743, \"B 0\": null, \"B 1\": 2.5975562052137366, \"n_models\": 4.0, \"escape_std\": 0.2001671331113208}, {\"site\": \"2\", \"mutant\": \"A\", \"escape\": 3.6192709663506637, \"epitope\": \"epitope 1\", \"A 0\": 3.89177300078208, \"A 1\": null, \"A 2\": 3.6192709663506637, \"B 0\": 3.125585310463836, \"B 1\": null, \"n_models\": 3.0, \"escape_std\": 0.3883783512660632}, {\"site\": \"4\", \"mutant\": \"K\", \"escape\": 0.3834415188257777, \"epitope\": \"epitope 1\", \"A 0\": 0.3834415188257777, \"A 1\": 0.9355390708060318, \"A 2\": 0.26682727510286663, \"B 0\": 0.05146720330082988, \"B 1\": 0.9031785237401092, \"n_models\": 5.0, \"escape_std\": 0.39403584052427915}, {\"site\": \"4\", \"mutant\": \"L\", \"escape\": 0.029876210878566956, \"epitope\": \"epitope 1\", \"A 0\": null, \"A 1\": 0.3132735169322751, \"A 2\": null, \"B 0\": 0.029876210878566956, \"B 1\": 0.005159148556627802, \"n_models\": 3.0, \"escape_std\": 0.1712013581760037}, {\"site\": \"4\", \"mutant\": \"Q\", \"escape\": 0.5135781212657464, \"epitope\": \"epitope 1\", \"A 0\": 0.925596638292661, \"A 1\": 0.44345289377955666, \"A 2\": 0.5135781212657464, \"B 0\": 0.6491440476147607, \"B 1\": 0.3614963440850427, \"n_models\": 5.0, \"escape_std\": 0.22079951184059773}, {\"site\": \"1\", \"mutant\": \"C\", \"escape\": 0.3006146806669343, \"epitope\": \"epitope 2\", \"A 0\": 0.4375872112626925, \"A 1\": 0.3965807272960261, \"A 2\": 0.2046486340378425, \"B 0\": null, \"B 1\": 0.14146417361702357, \"n_models\": 4.0, \"escape_std\": 0.14420628347773592}, {\"site\": \"2\", \"mutant\": \"A\", \"escape\": 0.29965467367452314, \"epitope\": \"epitope 2\", \"A 0\": 0.9636627605010293, \"A 1\": null, \"A 2\": 0.29965467367452314, \"B 0\": 0.20724287813818676, \"B 1\": null, \"n_models\": 3.0, \"escape_std\": 0.4126373948474744}, {\"site\": \"4\", \"mutant\": \"K\", \"escape\": 3.132963104392461, \"epitope\": \"epitope 2\", \"A 0\": 3.2917250380826646, \"A 1\": 3.346310916686017, \"A 2\": 3.121133832769295, \"B 0\": 2.9408098436506362, \"B 1\": 3.132963104392461, \"n_models\": 5.0, \"escape_std\": 0.15979056283813148}, {\"site\": \"4\", \"mutant\": \"L\", \"escape\": 2.0245481595728716, \"epitope\": \"epitope 2\", \"A 0\": null, \"A 1\": 2.0245481595728716, \"A 2\": null, \"B 0\": 1.956833224394711, \"B 1\": 2.07235649126018, \"n_models\": 3.0, \"escape_std\": 0.05804678316119469}, {\"site\": \"4\", \"mutant\": \"Q\", \"escape\": 3.7295772137298258, \"epitope\": \"epitope 2\", \"A 0\": 3.571036058197887, \"A 1\": 3.7295772137298258, \"A 2\": 3.6844398656469153, \"B 0\": 3.7784872826479754, \"B 1\": 4.104131938247697, \"n_models\": 5.0, \"escape_std\": 0.2001217829541086}, {\"site\": \"1\", \"mutant\": \"M\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"2\", \"mutant\": \"G\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"4\", \"mutant\": \"A\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"1\", \"mutant\": \"M\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"2\", \"mutant\": \"G\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}, {\"site\": \"4\", \"mutant\": \"A\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"A 0\": 0.0, \"A 1\": 0.0, \"A 2\": 0.0, \"B 0\": 0.0, \"B 1\": 0.0, \"n_models\": null, \"escape_std\": null}], \"data-a7d600054b448517d77aab4449a3c18a\": [{\"site\": \"1\", \"wildtype\": \"M\", \"_stat_site_order\": 0}, {\"site\": \"2\", \"wildtype\": \"G\", \"_stat_site_order\": 1}, {\"site\": \"4\", \"wildtype\": \"A\", \"_stat_site_order\": 2}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -3346,13 +3247,6 @@
    "execution_count": 15,
    "id": "17b2ad0d-0399-4b0d-8282-3400a998d3ef",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:18.271601Z",
-     "iopub.status.busy": "2023-07-19T19:40:18.271384Z",
-     "iopub.status.idle": "2023-07-19T19:40:18.325278Z",
-     "shell.execute_reply": "2023-07-19T19:40:18.324489Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:18.271584Z"
-    },
     "tags": []
    },
    "outputs": [],
@@ -3364,15 +3258,7 @@
    "cell_type": "code",
    "execution_count": 16,
    "id": "d21637c6-ebb8-481b-9a9e-9c313b4a90e3",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:18.326490Z",
-     "iopub.status.busy": "2023-07-19T19:40:18.326199Z",
-     "iopub.status.idle": "2023-07-19T19:40:18.367369Z",
-     "shell.execute_reply": "2023-07-19T19:40:18.366665Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:18.326472Z"
-    }
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -3446,13 +3332,6 @@
    "execution_count": 17,
    "id": "c9cd79cc-295a-461c-bcf0-adb7e57e12ca",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:18.368387Z",
-     "iopub.status.busy": "2023-07-19T19:40:18.368204Z",
-     "iopub.status.idle": "2023-07-19T19:40:18.474072Z",
-     "shell.execute_reply": "2023-07-19T19:40:18.473437Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:18.368371Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -3461,28 +3340,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-747641a11e704f77a57e7dddf3415eae.vega-embed {\n",
+       "  #altair-viz-572859ce9e194cc6914f33325f928c95.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-747641a11e704f77a57e7dddf3415eae.vega-embed details,\n",
-       "  #altair-viz-747641a11e704f77a57e7dddf3415eae.vega-embed details summary {\n",
+       "  #altair-viz-572859ce9e194cc6914f33325f928c95.vega-embed details,\n",
+       "  #altair-viz-572859ce9e194cc6914f33325f928c95.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-747641a11e704f77a57e7dddf3415eae\"></div>\n",
+       "<div id=\"altair-viz-572859ce9e194cc6914f33325f928c95\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-747641a11e704f77a57e7dddf3415eae\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-747641a11e704f77a57e7dddf3415eae\");\n",
+       "    if (outputDiv.id !== \"altair-viz-572859ce9e194cc6914f33325f928c95\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-572859ce9e194cc6914f33325f928c95\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -3518,12 +3397,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"labelLimit\": 500}}, \"data\": {\"name\": \"data-d70d59738f3d8e2ada1ce980ba47c0fb\"}, \"mark\": {\"type\": \"rect\", \"stroke\": \"black\"}, \"encoding\": {\"color\": {\"field\": \"r2\", \"scale\": {\"domain\": [0, 1], \"scheme\": \"yellowgreenblue\"}, \"type\": \"quantitative\"}, \"facet\": {\"columns\": 3, \"field\": \"epitope\", \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"r\", \"format\": \".3f\", \"type\": \"quantitative\"}, {\"field\": \"r2\", \"format\": \".3f\", \"type\": \"quantitative\"}, {\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"library_1\", \"type\": \"nominal\"}, {\"field\": \"replicate_1\", \"type\": \"quantitative\"}, {\"field\": \"library_2\", \"type\": \"nominal\"}, {\"field\": \"replicate_2\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_label_1\", \"title\": null, \"type\": \"nominal\"}, \"y\": {\"field\": \"_label_2\", \"title\": null, \"type\": \"nominal\"}}, \"height\": {\"step\": 15}, \"width\": {\"step\": 15}, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.8.0.json\", \"datasets\": {\"data-d70d59738f3d8e2ada1ce980ba47c0fb\": [{\"r\": 1.0, \"r2\": 1.0, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-0\", \"_label_2\": \"A-0\"}, {\"r\": 1.0, \"r2\": 1.0, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-0\", \"_label_2\": \"A-0\"}]}}, {\"mode\": \"vega-lite\"});\n",
+       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"labelLimit\": 500}}, \"data\": {\"name\": \"data-d70d59738f3d8e2ada1ce980ba47c0fb\"}, \"mark\": {\"type\": \"rect\", \"stroke\": \"black\"}, \"encoding\": {\"color\": {\"field\": \"r2\", \"scale\": {\"domain\": [0, 1], \"scheme\": \"yellowgreenblue\"}, \"type\": \"quantitative\"}, \"facet\": {\"columns\": 3, \"field\": \"epitope\", \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"r\", \"format\": \".3f\", \"type\": \"quantitative\"}, {\"field\": \"r2\", \"format\": \".3f\", \"type\": \"quantitative\"}, {\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"library_1\", \"type\": \"nominal\"}, {\"field\": \"replicate_1\", \"type\": \"quantitative\"}, {\"field\": \"library_2\", \"type\": \"nominal\"}, {\"field\": \"replicate_2\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_label_1\", \"title\": null, \"type\": \"nominal\"}, \"y\": {\"field\": \"_label_2\", \"title\": null, \"type\": \"nominal\"}}, \"height\": {\"step\": 15}, \"width\": {\"step\": 15}, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.16.3.json\", \"datasets\": {\"data-d70d59738f3d8e2ada1ce980ba47c0fb\": [{\"r\": 1.0, \"r2\": 1.0, \"epitope\": \"1\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-0\", \"_label_2\": \"A-0\"}, {\"r\": 1.0, \"r2\": 1.0, \"epitope\": \"2\", \"library_1\": \"A\", \"replicate_1\": 0, \"library_2\": \"A\", \"replicate_2\": 0, \"_label_1\": \"A-0\", \"_label_2\": \"A-0\"}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
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       "text/plain": [
@@ -3546,13 +3425,6 @@
    "execution_count": 18,
    "id": "8f31165f-71de-44d5-89ab-8aac85a41300",
    "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:18.475169Z",
-     "iopub.status.busy": "2023-07-19T19:40:18.474976Z",
-     "iopub.status.idle": "2023-07-19T19:40:18.488034Z",
-     "shell.execute_reply": "2023-07-19T19:40:18.487397Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:18.475152Z"
-    },
     "tags": []
    },
    "outputs": [
@@ -3621,43 +3493,35 @@
    "cell_type": "code",
    "execution_count": 19,
    "id": "e45b077a-e0f5-4d8a-a0a4-80eaf98cbe69",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:18.489154Z",
-     "iopub.status.busy": "2023-07-19T19:40:18.488854Z",
-     "iopub.status.idle": "2023-07-19T19:40:18.563482Z",
-     "shell.execute_reply": "2023-07-19T19:40:18.562766Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:18.489129Z"
-    }
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-3e3101d897bd45dbaf4c7abe6147ae8e.vega-embed {\n",
+       "  #altair-viz-eb84d7ba7468497d9b5c0a4f094a18fa.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-3e3101d897bd45dbaf4c7abe6147ae8e.vega-embed details,\n",
-       "  #altair-viz-3e3101d897bd45dbaf4c7abe6147ae8e.vega-embed details summary {\n",
+       "  #altair-viz-eb84d7ba7468497d9b5c0a4f094a18fa.vega-embed details,\n",
+       "  #altair-viz-eb84d7ba7468497d9b5c0a4f094a18fa.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-3e3101d897bd45dbaf4c7abe6147ae8e\"></div>\n",
+       "<div id=\"altair-viz-eb84d7ba7468497d9b5c0a4f094a18fa\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-3e3101d897bd45dbaf4c7abe6147ae8e\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-3e3101d897bd45dbaf4c7abe6147ae8e\");\n",
+       "    if (outputDiv.id !== \"altair-viz-eb84d7ba7468497d9b5c0a4f094a18fa\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-eb84d7ba7468497d9b5c0a4f094a18fa\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -3693,12 +3557,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false}}, \"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 18.75}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": null, \"scale\": {\"domain\": [\"1\", \"2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"activity_mean\", \"title\": \"activity_mean\", \"type\": \"quantitative\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}, {\"mark\": {\"type\": \"rule\", \"size\": 2}, \"encoding\": {\"color\": {\"value\": \"black\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_lower\", \"type\": \"quantitative\"}, \"x2\": {\"field\": \"_upper\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}], \"data\": {\"name\": \"data-b6ba616a701446645dcd238a30c2556a\"}, \"height\": {\"step\": 25}, \"width\": 110, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.8.0.json\", \"datasets\": {\"data-b6ba616a701446645dcd238a30c2556a\": [{\"epitope\": \"1\", \"activity_mean\": 2.5488135039273248, \"activity_median\": 2.5488135039273248, \"activity_std\": null, \"_lower\": null, \"_upper\": null}, {\"epitope\": \"2\", \"activity_mean\": 1.7151893663724196, \"activity_median\": 1.7151893663724196, \"activity_std\": null, \"_lower\": null, \"_upper\": null}]}}, {\"mode\": \"vega-lite\"});\n",
+       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false}}, \"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 18.75}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": null, \"scale\": {\"domain\": [\"1\", \"2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"activity_mean\", \"title\": \"activity_mean\", \"type\": \"quantitative\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}, {\"mark\": {\"type\": \"rule\", \"size\": 2}, \"encoding\": {\"color\": {\"value\": \"black\"}, \"tooltip\": [{\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"activity_mean\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_median\", \"format\": \".2f\", \"type\": \"quantitative\"}, {\"field\": \"activity_std\", \"format\": \".2f\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"_lower\", \"type\": \"quantitative\"}, \"x2\": {\"field\": \"_upper\"}, \"y\": {\"field\": \"epitope\", \"sort\": [\"1\", \"2\"], \"type\": \"nominal\"}}}], \"data\": {\"name\": \"data-b6ba616a701446645dcd238a30c2556a\"}, \"height\": {\"step\": 25}, \"width\": 110, \"$schema\": \"https://vega.github.io/schema/vega-lite/v5.16.3.json\", \"datasets\": {\"data-b6ba616a701446645dcd238a30c2556a\": [{\"epitope\": \"1\", \"activity_mean\": 2.5488135039273248, \"activity_median\": 2.5488135039273248, \"activity_std\": null, \"_lower\": null, \"_upper\": null}, {\"epitope\": \"2\", \"activity_mean\": 1.7151893663724196, \"activity_median\": 1.7151893663724196, \"activity_std\": null, \"_lower\": null, \"_upper\": null}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -3720,15 +3584,7 @@
    "cell_type": "code",
    "execution_count": 20,
    "id": "e12a5c30-7179-4279-9e8c-031b04ed8d22",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:18.566961Z",
-     "iopub.status.busy": "2023-07-19T19:40:18.566657Z",
-     "iopub.status.idle": "2023-07-19T19:40:18.598467Z",
-     "shell.execute_reply": "2023-07-19T19:40:18.597557Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:18.566943Z"
-    }
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -3916,43 +3772,35 @@
    "cell_type": "code",
    "execution_count": 21,
    "id": "0a899811-e216-4c47-97c5-c412162f9500",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:18.599808Z",
-     "iopub.status.busy": "2023-07-19T19:40:18.599424Z",
-     "iopub.status.idle": "2023-07-19T19:40:19.957972Z",
-     "shell.execute_reply": "2023-07-19T19:40:19.957274Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:18.599781Z"
-    }
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-421cc2f06f314d8d8ea9f413503c227a.vega-embed {\n",
+       "  #altair-viz-184e9655919144b5a6b0c51d38712232.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-421cc2f06f314d8d8ea9f413503c227a.vega-embed details,\n",
-       "  #altair-viz-421cc2f06f314d8d8ea9f413503c227a.vega-embed details summary {\n",
+       "  #altair-viz-184e9655919144b5a6b0c51d38712232.vega-embed details,\n",
+       "  #altair-viz-184e9655919144b5a6b0c51d38712232.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-421cc2f06f314d8d8ea9f413503c227a\"></div>\n",
+       "<div id=\"altair-viz-184e9655919144b5a6b0c51d38712232\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-421cc2f06f314d8d8ea9f413503c227a\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-421cc2f06f314d8d8ea9f413503c227a\");\n",
+       "    if (outputDiv.id !== \"altair-viz-184e9655919144b5a6b0c51d38712232\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-184e9655919144b5a6b0c51d38712232\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -3988,12 +3836,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false, \"labelOverlap\": \"parity\"}, \"padding\": 10}, \"vconcat\": [{\"data\": {\"name\": \"data-42e7f5dbd0282babbfecc80c452dbb2f\"}, \"mark\": {\"type\": \"rect\"}, \"encoding\": {\"color\": {\"value\": \"gray\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"nominal\"}], \"x\": {\"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}}, \"height\": 11, \"name\": \"view_10\", \"title\": \"site zoom bar\", \"width\": 500}, {\"layer\": [{\"mark\": {\"type\": \"line\", \"opacity\": 0.7, \"size\": 1}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": {\"orient\": \"left\"}, \"scale\": {\"domain\": [\"epitope 1\", \"epitope 2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"nominal\"}, {\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"_stat_site_val\", \"format\": \".3g\", \"title\": \"site escape\", \"type\": \"quantitative\"}, {\"field\": \"wildtype\", \"type\": \"nominal\"}], \"x\": {\"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}, \"y\": {\"field\": \"_stat_site_val\", \"scale\": {\"zero\": true}, \"title\": \"site escape\", \"type\": \"quantitative\"}}, \"name\": \"view_9\", \"transform\": [{\"lookup\": \"site\", \"from\": {\"data\": {\"name\": \"data-a7d600054b448517d77aab4449a3c18a\"}, \"key\": \"site\", \"fields\": [\"wildtype\", \"_stat_site_order\"]}}, {\"calculate\": \"if(isFinite(datum['escape']),datum['escape'],NaN)\", \"as\": \"escape\"}, {\"calculate\": \"if(isFinite(datum['']),datum[''],NaN)\", \"as\": \"\"}, {\"calculate\": \"if(isFinite(datum['n_models']),datum['n_models'],NaN)\", \"as\": \"n_models\"}, {\"calculate\": \"max(datum['escape'],floor_at_zero['floor'])\", \"as\": \"_stat\"}, {\"calculate\": \"false\", \"as\": \"_stat_hide\"}, {\"filter\": \"((datum['n_models'] >= (param_9['cutoff'] - 1e-06)) || (!isFinite(datum['n_models'])))\"}, {\"calculate\": \"if(datum['_stat_hide'],0.0,datum['_stat'])\", \"as\": \"_stat_not_hidden\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_hidden\", \"as\": \"_stat_site_max\"}], \"groupby\": [\"site\"]}, {\"filter\": \"((datum['_stat_site_max'] >= (param_10['cutoff'] - 1e-06)) || (!isFinite(datum['_stat_site_max'])))\"}, {\"calculate\": \"(datum.wildtype !== datum.mutant)\", \"as\": \"_stat_not_wildtype\"}, {\"joinaggregate\": [{\"op\": \"max\", \"field\": \"_stat_not_wildtype\", \"as\": \"_stat_site_has_non_wildtype\"}], \"groupby\": [\"site\"]}, {\"filter\": \"datum['_stat_site_has_non_wildtype']\"}, {\"filter\": {\"param\": \"param_12\"}}, {\"filter\": \"((datum.wildtype !== datum.mutant) && (!datum['_stat_hide']))\"}, {\"aggregate\": [{\"op\": \"sum\", \"field\": \"_stat\", \"as\": \"_stat_sum\"}, {\"op\": \"mean\", \"field\": \"_stat\", \"as\": \"_stat_mean\"}, {\"op\": \"max\", \"field\": \"_stat\", \"as\": \"_stat_max\"}, {\"op\": \"min\", \"field\": \"_stat\", \"as\": \"_stat_min\"}], \"groupby\": [\"site\", \"wildtype\", \"_stat_site_order\", \"epitope\"]}, {\"fold\": [\"_stat_sum\", \"_stat_mean\", \"_stat_max\", \"_stat_min\"], \"as\": [\"_stat_site_stat\", \"_stat_site_val\"]}, {\"filter\": {\"param\": \"site_stat\"}}, {\"calculate\": \"true\", \"as\": \"_stat_show_line\"}, {\"filter\": {\"param\": \"param_11\"}}]}, {\"mark\": {\"type\": \"circle\", \"opacity\": 0.7}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": {\"orient\": \"left\"}, \"scale\": {\"domain\": [\"epitope 1\", \"epitope 2\"], \"range\": [\"#0072B2\", \"#CC79A7\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"nominal\"}, {\"field\": \"epitope\", \"type\": \"nominal\"}, {\"field\": \"_stat_site_val\", \"format\": \".3g\", \"title\": \"site escape\", \"type\": \"quantitative\"}, {\"field\": 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\"Q\", \"escape\": 0.925596638292661, \"epitope\": \"epitope 1\", \"\": 0.925596638292661, \"n_models\": 1.0}, {\"site\": \"1\", \"mutant\": \"C\", \"escape\": 0.4375872112626925, \"epitope\": \"epitope 2\", \"\": 0.4375872112626925, \"n_models\": 1.0}, {\"site\": \"2\", \"mutant\": \"A\", \"escape\": 0.9636627605010293, \"epitope\": \"epitope 2\", \"\": 0.9636627605010293, \"n_models\": 1.0}, {\"site\": \"4\", \"mutant\": \"K\", \"escape\": 3.2917250380826646, \"epitope\": \"epitope 2\", \"\": 3.2917250380826646, \"n_models\": 1.0}, {\"site\": \"4\", \"mutant\": \"Q\", \"escape\": 3.571036058197887, \"epitope\": \"epitope 2\", \"\": 3.571036058197887, \"n_models\": 1.0}, {\"site\": \"1\", \"mutant\": \"M\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"\": 0.0, \"n_models\": null}, {\"site\": \"2\", \"mutant\": \"G\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"\": 0.0, \"n_models\": null}, {\"site\": \"4\", \"mutant\": \"A\", \"escape\": 0.0, \"epitope\": \"epitope 1\", \"\": 0.0, \"n_models\": null}, {\"site\": \"1\", \"mutant\": \"M\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"\": 0.0, \"n_models\": null}, {\"site\": \"2\", \"mutant\": \"G\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"\": 0.0, \"n_models\": null}, {\"site\": \"4\", \"mutant\": \"A\", \"escape\": 0.0, \"epitope\": \"epitope 2\", \"\": 0.0, \"n_models\": null}], \"data-afcf848cff8c29597107b52a4ea80b52\": [{\"site\": \"1\", \"wildtype\": \"M\", \"escape_std\": null, \"_stat_site_order\": 0}, {\"site\": \"2\", \"wildtype\": \"G\", \"escape_std\": null, \"_stat_site_order\": 1}, {\"site\": \"4\", \"wildtype\": \"A\", \"escape_std\": null, \"_stat_site_order\": 2}]}}, {\"mode\": \"vega-lite\"});\n",
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       "text/plain": [
@@ -4015,15 +3863,7 @@
    "cell_type": "code",
    "execution_count": 22,
    "id": "1eda7a75-87b0-4a40-800a-31d2a6f06c60",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2023-07-19T19:40:19.960686Z",
-     "iopub.status.busy": "2023-07-19T19:40:19.960158Z",
-     "iopub.status.idle": "2023-07-19T19:40:20.006991Z",
-     "shell.execute_reply": "2023-07-19T19:40:20.006277Z",
-     "shell.execute_reply.started": "2023-07-19T19:40:19.960650Z"
-    }
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -4553,7 +4393,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,